I like this concept, my thoughts are that with mewtwo being so attached to the Mc, there's a psychic link, so if she tries to "read" the egg, the link may impact the manaphy inside, taking aspects of their personality or maybe just having them jump from maturity. Shit, they could just be talking to the MC from the egg at the start of the chapter, whi would then hatch once all the pokemon in the chapter are obtained, so there's a rapid progression in maturity.
With the link, she can use the mc's senses to perceive the world while in the egg, maybe occasionally take control of limbs for comedic effect, like making the intrusive thoughts win.
Regardless of what you choose to do, I'll support you all the way homie.